Free books do not get to be on your purchased list forever. If you delete the books on your device, it will delete in the desktop app, and unless it is still free, you may never see it again. I keep ePUB backups.

I think Free kepubs never show up in purchased in the first place.. They only appear in the 'reading now' section and stay there till you erase them. Only way to get them back is to re-add them to your 'reading now' if it is still available as a free book at kobo.com.